For almost six years, the US authorities prohibited Muslim scholar Tariq Ramadan from travelli8ng to the United States, but now the secretary of state, Hillary Clinton, has signed an order effectively lifting the Bush-era ban for Ramadan, a visiting fellow at St Antony's College Oxford.

"Both the president and the secretary of state have made it clear that the US government is pursuing a new relationship with Muslim communities based on mutual interest and mutual respect," said state department spokesman Darby Holladay in a statement. "We'll let that action speak for itself."

Jameel Jafaar, Ramadan's American Civil Liberties Union lawyer said that the state department recognised the original exclusion was based on "political views." "We see secretary Clinton's decision as a recognition that the (exclusion was) illegitimate to begin with."

Since 2006, the American Civil Liberties Union has been fighting a lawsuit against the state department and the department of homeland security to challenge the visa ban on the Swiss-born Ramadan.

Plaintiffs the American Academy of Religion, Pen American Centre, and the American Association of University Professors were quick to laud the move. "The state department puts an end to one of the more shameful episodes in recent American history – the practice of preventing invited foreign scholars on the basis of their political beliefs," said Cary Nelson, president of the American Association of University Professors.

Ibrahim Hooper, the spokesperson for Council on American-Islamic Relations said in the case of Ramadan, "you're not talking about some far out extremist here, you're talking about somebody who is the mainstream of Muslim thought, who is critical of American foreign policy."

US immigration authorities first withheld Ramadan's visa allowing entry into the country in July 2004 when he was offered a tenured teaching position at the University of Notre Dame in Indiana. In 2006, Ramadan was denied a new visa.

The government alleged that from 1998 to 2002, Ramadan contributed around $1,300 to a Swiss-based charity, the Association de Secours Palestinien, which the US claimed was allied with Hamas.

In July of this year the ACLU prevailed against the Obama administration in a US appeals court decision, sending it back down to the district court.

Ramadan in a statement said he felt vindicated: the accusations "were nothing more than a pretense to prohibit me from speaking critically about American government policy on American soil." He said that "I am pleased to be able to go back to the states. Pleased, as well, that my name has been definitely cleared."

Ramadan's supporters were "very, very, happy" in the words of Abdou Rahman Kahim – executive member of the group Muslim Presence which holds Ramadan as a mentor. "We have been waiting for a long time," said Kahim from Ottawa, calling Ramadan "the best person to say we don't have a clash of civilisations, we have a clash of perceptions."

But there are those in the United States waiting to confront Ramadan.

Dr M Zuhdi Jasser, chairman of the board of the American Islamic Forum for democracy said that secretary Clinton "gave fuel to global Islamists who make specious claims attacking American foreign policy."

"As a Muslim, I don't believe that a majority of Muslims agree with Ramadan," says Jasser. "Ultimately I hope and pray if he gets more exposure in the United States that we really start to have a public discourse not between Tariq Ramadan and non-Muslims, but between Tariq Ramadan and Muslims that separate mosque and state that are looking to modernize Islam ... and truly having public discussions about the harm and the threat of political Islam and it's contribution to terror."

The order given by secretary Clinton also applied to Professor Adam Habib, a vice-chancellor of research, innovation and advancement at the University of Johannesburg who has been a vocal critic of the war in Iraq and some US terrorism-related activities.

The ACLU's Melissa Goodman said "the Obama administration should now conduct a broader review of visas denied under the Bush administration, reverse the exclusions of others who were barred because of their political beliefs and retire the practice of ideological exclusion for good."

"I hope it is only a start, Ramadan said. "Adam and myself, we are only symbols now we need a American vision and constructive policy towards the Muslims. It is high time to move from words to a comprehensive move through actions, institutionalisation, and effectiveness of this new relationship. I hope to be part of that move."